If you haven't noticed, my favorite tools these days are MSAmanda 2.0 (CharmeRT enabled so I can second search each spectra -- and then look at it in PD or MS2Go) and MetaMorpheus. We're generating new conclusions and new inspiration from the two of them all the time!
The drawback of the two is that there is still a lot of low res MS/MS out there. PRIDE is full of it! So are like 15 hard drives here! Both engines can process these spectra, but neither is ideal for it. It totally makes sense. If you're trying to confirm PTMs, you don't want to do that in ion trap MS/MS if you don't have to, right? It's so much easier and more confident in high res. (Both engines do more than this, of course, but that's primarily why I'm firing them up.)
However, if you've got 900 low res MS/MS files that you've acquired over the last 10 years or so and you've been dying for the software to get better so that you can look indiscriminately in those files for a ton of different PTMs in it using free software....you should be VERY interested in the new MetaMorpheus update!
If you don't have the software -- you can get it here.
P.S. What the heck is dioxidation on Tryptophan?!?!? And why are really nice looking spectra appearing as super abundant in these weird cells with the metabolic defects?!?!?
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